Crystal Structure of Inhibitor JNJ-2408068 in Complex with Prefusion RSV F Glycoprotein

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Molecular mechanism of respiratory syncytial virus fusion inhibitors.

Battles, M.B.Langedijk, J.P.Furmanova-Hollenstein, P.Chaiwatpongsakorn, S.Costello, H.M.Kwanten, L.Vranckx, L.Vink, P.Jaensch, S.Jonckers, T.H.Koul, A.Arnoult, E.Peeples, M.E.Roymans, D.McLellan, J.S.

(2016) Nat Chem Biol 12: 87-93

  • DOI: https://doi.org/10.1038/nchembio.1982
  • Primary Citation of Related Structures:  
    5EA3, 5EA4, 5EA5, 5EA6, 5EA7, 5EA8

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. Here we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.

  • Organizational Affiliation

    Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion glycoprotein F0A [auth F]568Human respiratory syncytial virus A2Mutation(s): 7 
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2))
Explore P03420 
Go to UniProtKB:  P03420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03420
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5NK

Download Ideal Coordinates CCD File 
I [auth F]2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol
C22 H30 N6 O
Query on NHE

Download Ideal Coordinates CCD File 
C8 H17 N O3 S
Query on SO4

Download Ideal Coordinates CCD File 
C [auth F]
D [auth F]
E [auth F]
G [auth F]
C [auth F],
D [auth F],
E [auth F],
G [auth F],
H [auth F]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
5NK BindingDB:  5EA3 EC50: 0.16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.11α = 90
b = 170.11β = 90
c = 170.11γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Charles H. Hood FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description